git clone

[Blosers]

Ask away!

nextflow.log pore-c.err.txt pore-c.out.txt pore-c.err.txt Hello,

I used git clone to download the relevant files and have also added the path to the .bashrc file. I created a new environment for the software and downloaded Nextflow. However, I still encountered issues when running it. Here are my commands:

!/bin/bash

SBATCH --job-name=pore-c

SBATCH --partition=Par-2

SBATCH --nodes=1

SBATCH --ntasks-per-node=10

SBATCH --error=/home/dingyuanhao/zxl_work/red_dwarf/DNPII/pore-c/pore-c.err

SBATCH --output=/home/dingyuanhao/zxl_work/red_dwarf/DNPII/pore-c/pore-c.out

source ~/.bashrc conda activate pore-c

nextflow run epi2me-labs/wf-pore-c \ --bam '/home/dingyuanhao/zxl_work/red_dwarf/DNPII/red_dwarf.bam' \ --chunk_size 100 \ --cutter 'DPNII' \ --hi_c true \ --mcool true \ --mcool_resolutions '1000,5000,10000,50000,100000,1000000' \ --paired_end_maximum_distance 200 \ --paired_end_minimum_distance 100 \ --ref '/home/dingyuanhao/zxl_work/red_dwarf/HA-T2T.fasta' \ -profile standard

or:

!/bin/bash

SBATCH --job-name=pore-c

SBATCH --partition=Par-2

SBATCH --nodes=1

SBATCH --ntasks-per-node=10

SBATCH --error=/home/dingyuanhao/zxl_work/red_dwarf/DNPII/pore-c/pore-c.err

SBATCH --output=/home/dingyuanhao/zxl_work/red_dwarf/DNPII/pore-c/pore-c.out

source ~/.bashrc conda activate pore-c

nextflow run /home/dingyuanhao/zxl_software/wf-pore-c \ --bam '/home/dingyuanhao/zxl_work/red_dwarf/DNPII/red_dwarf.bam' \ --chunk_size 100 \ --cutter 'DPNII' \ --hi_c true \ --mcool true \ --mcool_resolutions '1000,5000,10000,50000,100000,1000000' \ --paired_end_maximum_distance 200 \ --paired_end_minimum_distance 100 \ --ref '/home/dingyuanhao/zxl_work/red_dwarf/HA-T2T.fasta' \ -profile standard

.nextflow.log

[sarahjeeeze]

Hey looks like your input cmd is truncated try add newlines in cmd eg.

nextflow run epi2me-labs/wf-pore-c \
--bam '/home/dingyuanhao/zxl_work/red_dwarf/DNPII/red_dwarf.bam' \
--chunk_size 100 \
--cutter 'DPNII' \ 
... etc

[Blosers]

嘿，看起来你的输入 cmd 被截断了，尝试在 cmd 中添加换行符，例如。

nextflow run epi2me-labs/wf-pore-c \
--bam '/home/dingyuanhao/zxl_work/red_dwarf/DNPII/red_dwarf.bam' \
--chunk_size 100 \
--cutter 'DPNII' \ 
... etc

Sorry, there may be a flaw in the command I uploaded. Each line of the command displayed in my personal Linux port contains a line break: "Nextflow run/home/dingyuanhao/zxl_stoftware/wf-pore-c \ --Fastq/home/dingyuanhao/zxlw_work/red-dwarf/DNPII/pore-c/hic_data \, etc

[Blosers]

nextflow run epi2me-labs/wf-pore-c \ --bam '/home/dingyuanhao/zxl_work/red_dwarf/DNPII/red_dwarf.bam' \ --chunk_size 100 \ --cutter 'DPNII' \ ... etc

我在离线和在线两个版本都曾尝试过，但是最终输出的报错结果都是一样的。